Thermo-Sensitive Spikelet Defects 1 acclimatizes rice spikelet initiation and development to high temperature.

Crop reproductive development is vulnerable to heat stress, and the genetic modulation of thermotolerance during the reproductive phase, especially the early stage, remains poorly understood. We isolated a Poaceae-specific FAR-RED ELONGATED HYPOCOTYLS3 (FHY3)/FAR-RED IMPAIRED RESPONSE1 (FAR1)family transcription factor, Thermo-sensitive Spikelet Defects 1 (TSD1), derived from transposase in rice (Oryza sativa) TSD1 was highly expressed in spikelets, induced by heat, and specifically enhanced the thermotolerance of spikelet morphogenesis. Disrupting TSD1 did not affect vegetative growth but markedly retarded spikelet initiation and development, as well as caused varying degrees of spikelet degeneration, depending on the temperature. Most tsd1 spikelets were normal at low temperature but gradually degenerated as temperature increased, and all disappeared at high temperature, leading to naked branches. TSD1 directly promoted the transcription of YABBY1 and YABBY3 and could physically interact with YABBY1 and three TOB proteins, YABBY5, YABBY4, and YABBY3. These YABBY proteins can form either homodimers or heterodimers and play an important role in spikelet morphogenesis, similar to TSD1. Notably, the knockout mutant yab5-ko and double mutant tsd1 yab5-ko resembled tsd1 in spikelet appearance and response to temperature, indicating that these genes likely participate in spikelet development through the cooperative TSD1-YABBY module. These findings reveal a distinctive function of FHY3/FAR1 family genes and a unique TSD1-YABBY complex to acclimate spikelet development to high temperature in rice, providing insight into the regulating pathway of enhancing thermotolerance in plant reproductive development.

RETINOBLASTOMA-RELATED Genes Specifically Control Inner Floral Organ Morphogenesis and Pollen Development in Rice.

RETINOBLASTOMA-RELATED (RBR) is an essential gene in plants, but its molecular function outside of its role in cell cycle entry remains poorly understood. We characterized the functions of OsRBR1 and OsRBR2 in plant growth and development in rice using both forward- and reverse-genetics methods. The two genes were coexpressed and performed redundant roles in vegetative organs but exhibited separate functions in flowers. OsRBR1 was highly expressed in the floral meristem and regulated the expression of floral homeotic genes to ensure floral organ formation. Mutation of OsRBR1 caused loss of floral meristem identity, resulting in the replacement of lodicules, stamens, and the pistil with either a panicle-like structure or whorls of lemma-like organs. OsRBR2 was preferentially expressed in stamens and promoted pollen formation. Mutation of OsRBR2 led to deformed anthers without pollen. Similar to the protein interaction between AtRBR and AtMSI1 that is essential for floral development in Arabidopsis, OsMSI1 was identified as an interaction partner of OsRBR1 and OsRBR2. OsMSI1 was ubiquitously expressed and appears to be essential for development in rice (Oryza sativa), as the mutation of OsMSI1 was lethal. These results suggest that OsRBR1 and OsRBR2 function with OsMSI1 in reproductive development in rice. This work characterizes further functions of RBRs and improves current understanding of specific regulatory pathways of floral specification and pollen formation in rice.

Dwarf and deformed flower 1, encoding an F-box protein, is critical for vegetative and floral development in rice (Oryza sativa L.).

Recent studies have shown that F-box proteins constitute a large family in eukaryotes, and play pivotal roles in regulating various developmental processes in plants. However, their functions in monocots are still obscure. In this study, we characterized a recessive mutant dwarf and deformed flower 1-1 (ddf1-1) in Oryza sativa (rice). The mutant is abnormal in both vegetative and reproductive development, with significant size reduction in all organs except the spikelet. DDF1 controls organ size by regulating both cell division and cell expansion. In the ddf1-1 spikelet, the specification of floral organs in whorls 2 and 3 is altered, with most lodicules and stamens being transformed into glume-like organs and pistil-like organs, respectively, but the specification of lemma/palea and pistil in whorls 1 and 4 is not affected. DDF1 encodes an F-box protein anchored in the nucleolus, and is expressed in almost all vegetative and reproductive tissues. Consistent with the mutant floral phenotype, DDF1 positively regulates B-class genes OsMADS4 and OsMADS16, and negatively regulates pistil specification gene DL. In addition, DDF1 also negatively regulates the Arabidopsis LFY ortholog APO2, implying a functional connection between DDF1 and APO2. Collectively, these results revealed that DDF1, as a newly identified F-box gene, is a crucial genetic factor with pleiotropic functions for both vegetative growth and floral organ specification in rice. These findings provide additional insights into the molecular mechanism controlling monocot vegetative and reproductive development.

Glucan Synthase-like 2 is Required for Seed Initiation and Filling as Well as Pollen Fertility in Rice.

BACKGROUND: The Glucan synthase-like (GSL) genes are indispensable for some important highly-specialized developmental and cellular processes involving callose synthesis and deposition in plants. At present, the best-characterized reproductive functions of GSL genes are those for pollen formation and ovary expansion, but their role in seed initiation remains unknown. RESULTS: We identified a rice seed mutant, watery seed 1-1 (ws1-1), which contained a mutation in the OsGSL2 gene. The mutant produced seeds lacking embryo and endosperm but filled with transparent and sucrose-rich liquid. In a ws1-1 spikelet, the ovule development was normal, but the microsporogenesis and male gametophyte development were compromised, resulting in the reduction of fertile pollen. After fertilization, while the seed coat normally developed, the embryo failed to differentiate normally. In addition, the divided endosperm-free nuclei did not migrate to the periphery of the embryo sac but aggregated so that their proliferation and cellularization were arrested. Moreover, the degeneration of nucellus cells was delayed in ws1-1. OsGSL2 is highly expressed in reproductive organs and developing seeds. Disrupting OsGSL2 reduced callose deposition on the outer walls of the microspores and impaired the formation of the annular callose sheath in developing caryopsis, leading to pollen defect and seed abortion. CONCLUSIONS: Our findings revealed that OsGSL2 is essential for rice fertility and is required for embryo differentiation and endosperm-free nucleus positioning, indicating a distinct role of OsGSL2, a callose synthase gene, in seed initiation, which provides new insight into the regulation of seed development in cereals.

Characterization of Osmads6-5, a null allele, reveals that OsMADS6 is a critical regulator for early flower development in rice (Oryza sativa L.).

AGL6-clade genes are a subfamily of MADS-box genes and preferentially expressed in floral organs. OsMADS6 and OsMADS17 are two AGL6-like genes in rice. OsMADS17 has been shown to play a minor role in floral development and appears to result from a duplication of OsMADS6. OsMADS6 was initially named as MFO1 for mosaic floral organs based on its moderate mutant phenotypes. So far, four moderate or weak mutant alleles of OsMADS6 have been described, providing valuable insights into its role in flower development. Here, we report a null allele of OsMADS6 (Osmads6-5), which exhibited a strong mutant phenotype in spikelet without affecting vegetative traits, causing all floral organs except lemma homeotically transformed into lemma-like organs (LLOs) as well as an indeterminate floral meristem, thus resulting in a mutant floret consisting of reiterating whorls of lemma and LLOs. In consistently, over-expression of OsMADS6 led to additional lodicule-, stamen- and carpel-like organs. Expression analysis showed that OsMADS6 controls the formation of the incipient primordia of lodicule, stamen and carpel via regulating the expression of class B, C and SEP-like MADS-box genes. Taken together, our results revealed that OsMADS6 acts as a critical regulator for early flower development in rice and provide novel insights into the molecular mechanism of OsMADS6.

LUX ARRHYTHMO Interacts With ELF3a and ELF4a to Coordinate Vegetative Growth and Photoperiodic Flowering in Rice.

The evening complex (EC) plays a critical role in photoperiod flowering in Arabidopsis. Nevertheless, the underlying functions of individual components and coordinate regulation mechanism of EC genes in rice flowering remain to be elucidated. Here, we characterized the critical role of LUX ARRHYTHMO (LUX) in photoperiod perception and coordinating vegetative growth and flowering in rice. Non-functional alleles of OsLUX extremely extended vegetative phase, leading to photoperiod-insensitive late flowering and great increase of grain yield. OsLUX displayed an obvious diurnal rhythm expression with the peak at dusk and promoted rice flowering via coordinating the expression of genes associated with the circadian clock and the output integrators of photoperiodic flowering. OsLUX combined with OsELF4a and OsELF3a or OsELF3b to form two ECs, of which the OsLUX-OsELF3a-OsELF4a was likely the dominant promoter for photoperiodic flowering. In addition, OsELF4a was also essential for promoting rice flowering. Unlike OsLUX, loss OsELF4a displayed a marginal influence under short-day (SD) condition, but markedly delayed flowering time under long-day (LD) condition. These results suggest that rice EC genes share the function of promoting flowering. This is agreement with the orthologs of SD plant, but opposite to the counterparts of LD species. Taken together, rice EC genes display similar but not identical function in photoperiodic flowering, probably through regulating gene expression cooperative and independent. These findings facilitate our understanding of photoperiodic flowering in plants, especially the SD crops.

Knockdown of NtMed8, a Med8-like gene, causes abnormal development of vegetative and floral organs in tobacco (Nicotiana tabacum L.).

Med8, a subunit of mediator complex, has proved to possess crucial functions in many organisms from yeast to human. In plant, the med8 mutant of Arabidopsis thaliana displayed delayed anthesis and increased number of leaves during the vegetative period. However, the roles of Med8 in other flowering plants are still unknown. To investigate the function of Med8 ortholog in tobacco (Nicotiana tabacum L.; named as NtMed8), we created transgenic tobacco plants with repressed NtMed8 expression mediated by RNA interference (RNAi). Compared with the wild type, the NtMed8-RNAi plants exhibited: more leaves with smaller but thicker blades; larger cells and vascular bundles with lower stomata density in leaves; swelled chloroplasts with thicker and lumen-enlarged thylakoids; weaker root system with fewer lateral roots; larger flowers and floral organs; flowering earlier under long day, but later under short day conditions; and male sterile with larger but less germinable pollens. In addition, quantitative RT-PCR indicated that NtMed8 is expressed in both vegetative and floral tissues. Subcellular localization analysis by transient expression of fusion protein in Nicotiana benthamiana leaves showed that NtMed8 was located in both plasma membrane and nucleus. These results suggest that NtMed8 plays important roles in both vegetative and reproductive development, and the function of Med8 appears to be, at least partially, conserved in flowering plants.

[Genetic analysis and gene mapping of DDF1, a pleiotropic gene involving in both vegetable and reproductive growth in rice].

There are many pleiotropic genes playing key roles in regulating both vegetative growth and reproductive development in plants. A dwarf mutant of rice with deformed flowers, named as ddf1, was identified from indica rice breeding lines. Genetic analysis indicated that ddf1 was resulted from the recessive mutation of a single gene, temporarily named as DDF1. This result suggested that DDF1 is a pleiotropic gene, which controls both vegetative growth and reproductive development in rice. To map this gene, an F2 population was developed by crossing the ddf1 heterozygote with the tropical japonica rice variety DZ60. By means of bulked segregant analysis and small population-based linkage analysis using the published RM-series rice SSR markers, DDF1 was preliminarily mapped in a region between markers RM588 and RM587 on chromosome 6 with the genetic distances of 3.8 cM and 2.4 cM to the two markers, respectively. By developing new SSR markers in this interval according to the published rice genome sequence, we further mapped DDF1 in a 165 kb interval. The results will facilitate cloning of DDF1.

Molecular cloning and functional characterization of OsJAG gene based on a complete-deletion mutant in rice (Oryza sativa L.).

In this article, we report an independent work of positional cloning and functional characterization of OsJAG gene in rice. The merit of our work is that we used a genuine null mutant, in which the wild-type allele was completely deleted. This allowed us to identify the mutant phenotypes accurately without the interference of residual function of the target gene. OsJAG is an important gene with pleiotropy, expressing almost throughout the plant and acting in both vegetative phase and reproductive phase. But its main and crucial roles are in regulating the development of all floral organs, especially in specifying the identity of stamens. Interestingly, OsJAG does not affect the number of floral organ primordial and so of floral organs in each whorl, suggesting that OsJAG does not influence the initiation of floral organ primordia, but affect the developmental fate of all floral organs after their primordia have initiated. Loss of OsJAG function results in maldevelopment of all floral organs, such as degenerated lemma and palea, elongated lodicules and deformed and sterile pistil. The stamen appears to be more sensitive to the mutation. All the six stamens in a mutant floret were thoroughly transformed into six pistil-like organs developed at the presumptive positions of the stamens in whorl 3.

Screening and analysis of proteins interacting with OsMADS16 in rice (Oryza sativa L.).

OsMADS16, a class B floral organ identity gene, plays a pivotal role in stamen formation in rice. To date, little is known about the interacting partners of OsMADS16 except for several MADS-box proteins. In this study, we constructed a high-quality cDNA library of young panicles (< 5 cm in length) and performed yeast two-hybrid (Y2H) screening using OsMADS16 as bait. Eleven candidate proteins interacting with OsMADS16 were identified by Y2H and validated by BiFC and Co-IP assays. Subcellular localization results further confirmed the possibility of the interactions of OsMADS16 with 10 of the candidate proteins in natural rice cells. Bioinformatics analysis indicated that these partners exerted various molecular, cellular and physiological functions. Some of them were known or likely to be related to reproductive events, such as stamen primordium initiation, differentiation and development (OsMADS2, OsMADS4 and OsCOP9) and pollen development (OsbHLH40 and Os6PGDH). Our results provide an important reference for further research on OsMADS16-mediated regulation mechanism on floral organ development and pollen formation.

[Genetic analysis and gene mapping of cold-induced seedling chlorosis in rice].

We found that the seedlings of indica rice cultivar Dular showed chlorosis but the seedlings of japonica rice cultivar Lemont remained green under natural low temperature in early spring. Using an F2 population of Lemont Dular, we found that the difference of cold tolerance at seedling stage between Dular and Lemont is controlled by a single major gene, with the chlorosis allele being recessive. We named the gene cisc(t). With the help of SSR markers, cisc(t) was mapped in a 5.5 cM interval between SSR markers RM257 and RM242 on chromosome 9.

Genetic analysis and mapping of gene fzp(t) controlling spikelet differentiation in rice.

A mutant of spikelet differentiation in rice called frizzle panicle (fzp) was discovered in the progeny of a cross between Oryza sativa ssp. indica cv. V20B and cv. Hua1B. The mutant exhibits normal plant morphology but has apparently fewer tillers. The most striking change in fzp is that its spikelet differentiation is completely blocked, with unlimited subsequent rachis branches generated from the positions where spikelets normally develop in wild-type plants. Genetic analysis suggests that fzp is controlled by a single recessive gene, which is temporarily named fzp(t). Based on its mutant phenotype, fzp(t) represents a key gene controlling spikelet differentiation. Some F(2) mutant plants derived from various genetic background appeared as the "middle type", suggesting that the action of fzp(t) is influenced by the presence of redundant, modifier or interactive genes. By using simple sequence repeat (SSR) markers and bulked segregant analysis (BSA) method, fzp(t) gene was mapped in the terminal region of the long arm of chromosome 7, with RM172 and RM248 on one side, 3.2 cM and 6.4 cM from fzp(t), and RM18 and RM234 on the other side, 23.1 cM and 26.3 cM from fzp(t), respectively. These results will facilitate the positional cloning and function studies of the gene.

[Towards the positional cloning of a spikelet identity gene frizzle panicle (FZP) in rice (Oryza sativa L.)].

FZP is a key gene for spikelet differentiation in rice. Mutation of the gene blocks the differentiation of spikelets and makes rachis branches develop unlimitedly. A mutant of the gene named frizzle panicle (fzp) was previously found from the high-generation progeny of a cross between two Oryza sativa ssp. indica rice varieties, V20B and Hua1B. With the mutant, FZP had been mapped to a chromosomal region of about 26.4 cM in width between two SSR (Simple Sequence Repeat) markers, RM172 and RM18, on chromosome 7. In this study, high-resolution mapping of the gene was carried out for the positional cloning of the gene. Two flanking SSR markers, NRM6 and NRM8, were identified, which are 0.2 cM and 1.0 cM apart from the target gene, respectively, bracketing the target gene within an interval of 1.2 cM or 144 kb. An APETALA2 (AP2)-domain like gene was found at the expected position of FZP. As AP2 is known to play an important role in the floral development, we took it as the most possible candidate of FZP. PCR analysis showed that the mutant allele of the AP2-domain like gene contains an insert of about 4 kb in length, suggesting that the gene is very likely FZP.

Toward the positional cloning of qBlsr5a, a QTL underlying resistance to bacterial leaf streak, using overlapping sub-CSSLs in rice.

Bacterial leaf steak (BLS) is one of the most destructive diseases in rice. Studies have shown that BLS resistance in rice is quantitatively inherited, controlled by multiple quantitative trait loci (QTLs). A QTL with relatively large effect, qBlsr5a, was previously mapped in a region of ∼ 380 kb on chromosome 5. To fine map qBlsr5a further, a set of overlapping sub-chromosome segment substitution lines (sub-CSSLs) were developed from a large secondary F2 population (containing more than 7000 plants), in which only the chromosomal region harboring qBlsr5a was segregated. By genotyping the sub-CSSLs with molecular markers covering the target region and phenotyping the sub-CSSLs with artificial inoculation, qBlsr5a was delimited to a 30.0-kb interval, in which only three genes were predicted. qRT-PCR analysis indicated that the three putative genes did not show significant response to the infection of BLS pathogen in both resistant and susceptible parental lines. However, two nucleotide substitutions were found in the coding sequence of gene LOC_Os05g01710, which encodes the gamma chain of transcription initiation factor IIA (TFIIAγ). The nucleotide substitutions resulted in a change of the 39th amino acid from valine (in the susceptible parent) to glutamic acid (in the resistant parent). Interestingly, the resistant parent allele of LOC_Os05g01710 is identical to xa5, a major gene resistant to bacterial leaf blight (another bacterial disease of rice). These results suggest that LOC_Os05g01710 is very possibly the candidate gene of qBlsr5a.